A multiscale spatiotemporal map of protein-RNA assemblies in human cells

RNA metabolism is dynamically orchestrated by RNA-binding proteins (RBPs) in different subcellular spaces. Aberrant regulation of the subcellular RNA-protein interactions leads to severe diseases, such as neural degenerations and cancers. Understanding the precise spatiotemporal dynamics of RBPs and their interacting networks in the steady state and upon perturbation is key to deciphering the cell function. We present the coRIC (compartmentalized RNA Interactome Capture) map, an experimental resource and analytical pipeline to study the subcellular dynamics of RBPs through multimodal dataset integration and machine learning. coRIC map successfully identified 1,768 RBPs, including previously underestimated RBPs, spanning 14 major subcellular regions. This map offered us the opportunity to delineate subcellular RBP features, their intermolecular and intercompartmental relationships. We have also defined the hierarchy of RBP complexes at multiple scales across the cell, uncovering previously unknown functions of multiple RBPs, such as IGF2BP1. Application of coRIC under the perturbations of DNA damage and ALS-related dipeptide repeats uncovered the cRBP dynamic changes in complex composition and subcellular distribution. Our work provides a new reference for systematically studying the subcellular RNA-protein interactions, which helps understand the RBP regulatory networks in RNA biology and disease.